Edinburgh Research Explorer Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Edinburgh Research Explorer Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
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通讯作者：
Frantz;Laurent Af Frantz;J. Schraiber;O. Madsen;H. Megens;M. Bosse;Yogesh Paudel;G. Semiadi
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作者：
Frantz;Laurent Af Frantz;J. Schraiber;O. Madsen;H. Megens;M. Bosse;Yogesh Paudel;G. Semiadi
背景：阐明物种形成的过程需要深入了解有关物种的进化历史。依赖于有限数量的遗传基因座的研究并不总是揭示实际的进化历史，并且经常混淆与物种发生和物种形成有关的推论。然而，全基因组数据可以通过提供一个几乎无偏的窗口来了解物种形成的模式和过程，从而克服这个问题。为了揭示物种形成过程的复杂性，我们对10只野猪的基因组进行了测序和分析，这些野猪在形态上或地理上代表了来自东南亚岛屿和大陆的猪属物种和亚种，以及一只非洲普通野猪。结果如下：我们的数据突出了过去周期性气候波动在促进种群扩散和隔离方面的重要性，从而导致世界上物种最丰富的地区之一的suids多样化。此外，混合物分析揭示了广泛的，内部和种间的基因流，解释了以前从有限数量的位点获得的相互矛盾的结果。我们表明，这些多个事件的基因流导致自然和人为介导的传播。结论：我们的研究结果表明，过去的气候波动和人类介导的易位在驱动和复杂化的过程中的物种在东南亚岛屿的重要性。这一案例研究表明，基因组学是一个强有力的工具，以破译一个属的进化历史，并揭示了物种形成过程的复杂性。
Background: Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results: Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions: Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.